I noticed another line on the link you included which may explain the absence of El Almirante: "The following is not a complete list of the foreign flag ships lost or damaged during World War II that were under the control of the War Shipping Administration. There were many others lost that did not carry any Americans in the merchant crew but did have U.S. Naval Armed Guard aboard. Data on these ships was not available."
Based on the information you provided, it seems that Company 357 probably referred to his initial class at Newport. If Seaman 1st Class Donovan subsequently attended USNAG training, his father must not have noted it on the form.
Two questions if I may:
1) Does a total training period of five months from entering the U.S. Navy to being aboard a ship as a member of USNAG make sense, or would it be too brief?
2) Assuming he was not USNAG (say, if he were simply being shipped to England for other duties as a passenger), is it likely that he would have ended up on a a Panamanian cargo ship as opposed to a transport or U.S. vessel? Thanks.